The Clean Water Act (CWA) authorizes the EPA to implement the National Pollutant Discharge Elimination System (NPDES), a program that prohibits any point source from discharging pollutants into “waters of the United States” unless they have an NPDES permit.[1,2]
Point sources are commonly understood to be factories or sewage treatment plants that discharge pollutants into waterways. But the CWA explicitly refers to “concentrated animal feeding operations” (CAFOs) as point sources.[3]
In defining what a makes a CAFO, the EPA established a size threshold (i.e., number of animals) on a facility where animals are kept and raised in confined conditions. But any animal feeding operation (AFO), regardless of size, that has been found to have discharged pollutants contributing to water impairment is designated a CAFO and thus deemed a “point source.” It is then also subject to NPDES permitting requirements.[4]
The EPA vests the NPDES permit program to state, tribal, and territorial governments to operate its permitting, administration, and enforcement. In states so authorized, the EPA retains oversight responsibilities. Currently 47 states and one territory are authorized to implement the NPDES program.[5]
The Clean Water Act, 33 U.S.C. § 1251 et seq.
40 CFR §122.1 EPA Administered Permit Programs: the National Pollutant Discharge Elimination
System, Subpart A – Definitions and General Program RequirementsThe Clean Water Act, Definitions 33 U.S.C. § 1362(14)[“The term “point source” means any discernible, confined and discrete conveyance, including but not limited to any pipe, ditch, channel, tunnel, conduit, well, discrete fissure, container, rolling stock, concentrated animal feeding operation, or vessel or other floating craft, from which pollutants are or may be discharged. This term does not include agricultural stormwater discharges and return flows from irrigated agriculture.”]
For CAFO regulatory definition, see Defining AFOs & CAFOs
U.S. EPA (2024) NPDES State Program Authority. https://www.epa.gov/npdes/npdes-state-program-authority
It is a license for a facility to discharge a specified amount of a pollutant into a receiving water under certain conditions. The permit contains limits on what can be discharged, requirements for monitoring and reporting, and other provisions intended to ensure that the discharge does not harm water quality.[1]
U.S. EPA (2024) National Pollutant Discharge Elimination System (NPDES), About NPDES. https://www.epa.gov/npdes/about-npdes
No. In what is known as the Waterkeeper case, a federal court ruled that the EPA cannot require all CAFOs have permits. The Court ruled that a permit is only required if an operation is, in fact, discharging a pollutant or it plans to discharge pollutants. In addition, the Waterkeeper decision established that an unpermitted CAFO can self-certify that it does not discharge or propose to discharge – a certification that is not reviewable by the federal or state permitting authority.[1,2]
Another federal court later vacated the rule that required a CAFO proposing to discharge first obtain a permit.[3] And the EPA revised the regulations again to require a CAFO have a permit only if there is an actual discharge of pollutants into navigable water.[4]
U.S. EPA (2008) Regulation and Effluent Limitations Guidelines for CAFOs in Response to the Waterkeeper Decision, 73 Fed. Reg. 70418, 70426. [“EPA has concluded that providing a voluntary option for unpermitted CAFOs to certify to the Director that the CAFO does not discharge or propose to discharge based on an objective assessment of the CAFO’s design, construction, operation, and maintenance is reasonable and appropriate for CAFOs.”] [“A CAFO’s no discharge certification is not subject to review by the permitting authority in order for it to become effective and the permitting authority is not required to make the certification available to the public for comment because the certification is not a permit application for which review is required under section 402 of the CWA.”]
For more information on the NPDES system and history, see NPDES for CAFOs
National Pork Producers Council v. EPA, 635 F.3d 738 (2011).
Leah Hurtgen Ziemba (2012) Federal CAFO Regulations Remove “Propose to Discharge” Permitting Requirement, National Law Review. And see, U.S. EPA (2024) Animal Feeding Operations – Regulations, Guidance, and Studies, Regulations 2012, Compiled CAFO Rule (July 30, 2012).
The EPA currently lists 6,174 CAFOs with NPDES permits. The agency reports that there are 21,179 EPA-defined CAFOs in the U.S.[1]
There are vast differences in state protocols for implementing NPDES permits. For instance, in Oregon (where 355 CAFOs have permits) the term “confined animal feeding operation” has no size threshold and is broadly defined to include slaughterhouses and fur farms. All operations that meet the Oregon definition are required to apply for a permit.[2] However, in Iowa where the EPA estimates there are more than 4,000 EPA-defined CAFOs, only 157 have permits. And in Indiana, Idaho, Arkansas, and New York where there are more than 2,380 EPA-defined CAFOs, none have permits.[3]
US EPA (May 2024) NPDES CAFO Permitting Status Report: National Summary, End year 2023. https://www.epa.gov/npdes/npdes-cafo-regulations-implementation-status-reports [“Reports include the total number of CAFOs, and the number of CAFOs with NPDES permits for each state.”]
Oregon Dept. of Agriculture, Chapter 603, Confined Animal Feeding Operation Program. https://secure.sos.state.or.us/oard/displayDivisionRules.action?selectedDivision=2751
NPDES CAFO Permitting Status Report, End year 2023
Only if a CAFO is operating with a permit (which confers authority on the EPA to regulate). In that case, the rules of allowable discharge apply to its entire production area. EPA regulations have determined that all manure storage areas such as lagoons, sheds, or pits are deemed part of the “production area” of an animal feeding operation. So, too, are animal confinement areas, storage for raw materials, and areas used in the handling and disposal of dead animals.[1,2]
Current regulations for permitted CAFOs generally prohibit discharge of manure, litter, or wastewater into U.S. waters from the production area, unless precipitation causes an overflow resulting in such a discharge. In that case, the overflow is permissible if the production area is “designed, constructed, operated and maintained to contain all manure, litter, and process wastewater including the runoff and the direct precipitation from a 25-year, 24-hour rainfall event.”[3,4]
EPA lacks the authority to regulate manure lagoons and other manure storage areas in CAFOs that do not have permits.
40 CFR § 412.31(a) Effluent limitations attainable by the application of the best practicable control technology currently available (BPT)
40 CFR § 412.2(h) Concentrated Animal Feeding Operations (CAFO) Point source category, General definitions
40 CFR § 412.31(a)
Note: If the CAFO is a dairy operation with >700 cows or a cattle operation with >1,000 cattle, routine visual inspections of the lagoons or manure pits are also required along with records of the inspections. 40 CFR § 412.37 Subpart C Dairy Cows and Cattle Other than Veal Calves, Additional measures
To a limited degree. Rules for land application of factory farm waste are addressed in the guidelines of Nutrient Management Plans (NMP). Any operation applying for an NPDES permit must submit a plan in order to obtain a permit, and if an operation meets the EPA definition of a Large CAFO it must maintain an NMP.[1] Thus, to the extent that NMPs are reviewable by the EPA, land application is ”regulated.”
A Nutrient Management Plan is a site-specific planning document that addresses conservation practices, and it includes “protocols to land apply manure, litter or process wastewater in accordance with site specific nutrient management practices that ensure appropriate agricultural utilization of the nutrients in the manure, litter or process wastewater.”[2] As would be expected by the term nutrient, NMP guidelines for land application of manure focus on the potential for pollution from nitrogen and phosphorus; other contaminants in manure such as pathogens, antibiotic and pesticide residues, hormones, and metals, are not addressed.[3,4]
In 1987, Congress removed land application of manure and wastewater from federal oversight when it amended the Clean Water Act to exempt “agricultural stormwater discharges” from the statutory definition of a point source, re-labeling agricultural runoff from fields as nonpoint sources.[5]
The EPA subsequently reasoned that Congress hadn’t meant to exclude any and all discharges of CAFO manure from land application areas regardless of how excessively the manure was applied. Thus, the agency established that all permits for CAFOS required a Nutrient Management Plan, and if a CAFO is complying with that plan, any remaining discharge not authorized by the permit is covered by the ‘‘agricultural stormwater discharge” exemption.[6]
While EPA regulations establish the minimum NMP requirements for permitted CAFOs, states may require more stringent requirements, and in many cases states have established additional requirements to address land application.[7]
40 CFR § 122.42(e) [Federal regulations do not require that unpermitted CAFOs implement a formal NMP. “However, for precipitation related discharges from the land application area to qualify as agricultural stormwater exempt from permit requirements, unpermitted CAFOs must develop and implement the nutrient management practices…” (U.S. EPA (2012) NPDES Permit Writers’ Manual for Concentrated Animal Feeding Operations, EPA 833-F-12-001, section 5.1.3]
40 CFR § 122.42(e)(1)(viii)
40 CFR § 123.36; 412.4(c)(1)
See, generally, U.S. EPA (2013) Literature Review of Contaminants in Livestock and Poultry Manure and Implications for Water Quality, EPA 820-R-13-002.
Clean Water Act 33 U.S.C. § 1362(14) Definitions [“This term (point source) does not include agricultural stormwater discharges and return flows from irrigated agriculture.”]
U.S. EPA (2003) National Pollutant Discharge Elimination System Permit Regulation and Effluent Limitation Guidelines and Standards for Concentrated Animal Feed Operations (CAFOs), 68 Fed. Reg. 7176, 7198.
NPDES Permit Writers’ Manual, p. 4-15.
There’s not a great deal of research on this topic, although there is evidence that farmers who implement NMP’s still over-apply nutrients. This is largely because the EPA’s regulations incorporate dual objectives in an NMP – that of achieving “realistic production goals, while minimizing nitrogen and phosphorus movement to surface waters.”[1]
CAFO operators set their own yield goals, which automatically creates an incentive to overestimate nutrients required.[2] As pointed out in a 2017 petition to the EPA, Food & Water Watch et al. writes, “The dual goals, expressed in EPA’s regulations and state technical standards, of maximizing production and minimizing pollution are often incompatible and when in doubt, state standards typically authorize operators to over‒apply animal wastes and other supplements in order to ensure that crops have sufficient nutrients to ensure optimal growth.”[3]
In addition, surveys have also found that many farmers do not follow the guidelines in their NMPs.[4,5] Reasons given in one survey: they didn’t trust nutrient recommendations of agricultural extensions, or they relied on fertilizer dealers to make nutrient determinations, and in general, believed conservation practices too time consuming.[6] A survey conducted in Indiana found that less than 3% saw nutrient pollution as severe problems in the area, and that “Livestock owners were more likely to say that sedimentation/silt, nitrates, and phosphorus are not water pollution problems in their area.”[7]
Overall, it is likely that farmers who do have NMPs are less likely to over-apply nutrients than those who don’t.[8] However, there is no requirement to monitor pollutants in runoff water from land application areas or underground discharges from waste containment structures.[9] Thus, there is no way to ensure the CAFO is complying with permit requirements.[10]
Best management practices (BMPs) for land application of manure, litter, and process wastewater, Nutrient Management Plan, 40 CFR Part 412, § 412.4(c)(1).
Long, C.M., et al., (2018) Use of manure nutrients from concentrated animal feeding operations, J. Great Lakes Res. Vol 44, Issue2, p. 4. [Study finding farmers “over-estimating crop yields in calculating plant nutrient requirements (67% of all cases) and applying beyond what is allowed by state permits (26% of all cases).”]
Food & Water Watch, et al. vs. EPA, Petition to Revise the Clean Water Act Regulations for Concentrated Animal Feeding Operations (2017)
Osmond, D. L., et al., (2015) Farmers’ Use of Nutrient Management: Lessons from Watershed Case Studies, J. Environ. Qual. 44:382-390, Abstract. [“Results indicate farmers generally did not fully apply nutrient management plans or follow basic soil test recommendations even when they had them.”]
Ulrich-Schad, J.D., & Prokopy, L. S. (2015) 2014 Nutrient Management Survey-Executive Summary, Purdue University, Dept. of Forestry and Natural Resources, p. 5. [project funded by Indiana corn and soybean farmer checkoff funds]
Osmond, D. L., et al., (2015), p. 6.
Ulrich-Schad, J.D., & Prokopy, L. S. (2015), p. 4. & 10.
Shepard, R. (2005). Nutrient management planning: Is it the answer to better management? Journal of Soil and Water Conservation, 60(4), 171–176, p. 174.
U.S. EPA (2003) National Pollutant Discharge Elimination System Permit Regulation and Effluent Limitation Guidelines and Standards for Concentrated Animal Feed Operations (CAFOs), 68 Fed. Reg. 7176, 7217. [“In this final rule, EPA is continuing to reject imposing surface water monitoring requirements on CAFOs through the effluent guidelines because of concerns regarding the difficulty of designing and implementing through a national rule an effective surface water monitoring program.”]
This was pointed out in Food & Water Watch v. EPA, 13 F.4th 896 (9th Circ. 2021) [“The Idaho Permit forbids underground discharges from production areas and dry weather discharges from land application areas. However, the Permit contains no monitoring requirements for either kind of discharge. Because the Permit does not require monitoring that would ensure compliance with its effluent limitations, the EPA’s issuance of the Permit was arbitrary, capricious, and a violation of law.” pp. 26-27]
No. Industrial animal ag is most likely the single largest contributor to the pollution of U.S. waterways via manure discharge and land application, as well as excess fertilizer use on feed crops.[1] Ineffective laws and the lack of monitoring are the main reasons.[2]
Researchers from the U.S. Geological Survey note, “Nonpoint nutrient inputs, which are typically dominant in agricultural areas, have not been targeted by U.S. environmental laws in the same way as point discharges.”[3]
The EPA also acknowledges that “Many CAFOs are not regulated and continue to discharge without NPDES permits.”[4] Even CAFOs with permits are often engaging in land application practices in violation of permit restrictions.[5]
The EPA further concedes that “little data is available demonstrating the impacts of CAFOs specifically on ‘waters of the United States,’ particularly considering the agricultural stormwater exemption.”[6] This would seem to be a surprising concession in view of the EPA’s role under the Clean Water Act and the agency’s awareness that manure is a primary source of water pollution.[7]
As one legal critic stated, “one would be hard pressed to identify another industry with as poor an environmental record and as light a regulatory burden.”[8] Other researchers and analysts concur.[9-11]
See, Nutrient Pollution and Animal Ag Overview and Animal Ag Contributions to Water Pollution
For a comprehensive legal analysis of the EPA’s failure to regulate manure from factory farms, see, Emily Miller’s interview on The Animal Law Podcast, Mariann Sullivan host (November 27, 2024), “Animal Law Podcast 114: The Case of the Not-So-Clean Water Act.” https://www.ourhenhouse.org/alp114/ [Emily Miller is an attorney with Food & Water Watch – transcript on the site]
Stets, E. G., et al., (2020). Landscape drivers of dynamic change in water quality of US rivers. Environmental Science & Technology, 54(7), 4336-4343, p. 4339. [“…our results indicate that nutrient concentrations remain elevated in agricultural watersheds, which is known to be a pressing water quality problem and stands in contrast to the apparent progress in urban areas.”]
U.S. EPA (May 2022) EPA Legal Tools to Advance Environmental Justice, EPA Publication No. 360R22001, p. 75.
See above question on efficacy of nutrient management plans.
U.S. EPA (2023) Effluent Guidelines Program Plan 15, EPA-821-R-22-004, p. A-4.
U.S. EPA (2023) Estimated Animal Agriculture Nitrogen and Phosphorus from Manure. https://www.epa.gov/nutrientpollution/estimated-animal-agriculture-nitrogen-and-phosphorus-manure
Ruhl, J.B. (2000) Farms, Their Environmental Harms, and Environmental Law. Ecology Law Quarterly, 27(2), 263, p. 269. https://doi.org/10.15779/Z38C55S
Bonnet, C., et al., (2020). Viewpoint: Regulating meat consumption to improve health, the environment and animal welfare. Food Policy, 97, 101847, p. 4. [“However, the standard approach in economics recommends regulating pollution at the source, namely at the farm; yet, this is notoriously difficult in agriculture, as it requires detailed farm-level measurements of pollution. Moreover, agricultural pollution, such as water pollution, is typically plagued by the nonpoint source issue, which makes it difficult to identify the polluters and thus to regulate efficiently.”]
Glibert, P. (2020). From hogs to HABs: impacts of industrial farming in the US on nitrogen and phosphorus and greenhouse gas pollution. Biogeochemistry, 150(2), 139–180, p. 160. [“The historical balance that small farmers sustained between animal waste production and crops that fed both animals and people is still the notion that many have with respect to farming. This ingrained belief has resulted in agricultural operations having the privilege of exemptions of many provisions of environmental laws.”]
Lavaine, E., et al., (2020). Health, air pollution, and animal agriculture. Review of Agricultural, Food and Environmental Studies, 101(4), 517–528, p. 524. [“High-polluting sectors such as transport or energy have long been regulated; however, this is not the case of the agricultural sector, which has benefited from regulatory exemptions and low oversight.”]
In 2023, the EPA announced that it would undertake a study of CAFO production area and land application rates to see if revising the effluent limit guidelines (ELG) for nutrient management plans (NMP) is warranted.[1] This was in response to a 2017 lawsuit brought by several environmental groups in Food & Water Watch v. EPA.[2]
It is likely that this review will take quite a while as the agency points out that previous CAFO rulemakings spanned about 11 years.[3] It is also unclear – even if new ELGs are established – what effect they will have since they are guidelines for nutrient management plans only.
The Farm, Ranch, and Rural Communities Federal Advisory Committee (FRRCC), which offers policy advice to the EPA has created a subcommittee called the Animal Agriculture Water Quality Subcommittee. This committee will provide recommendations on how and if the agency should improve the NPDES program to “more effectively reduce nutrients and other types of water pollutants from Animal Feeding Operations.”[4]
U.S. EPA (2023) Effluent Guidelines Program Plan 15, EPA-821-R-22-004, p. 6-2.
Food & Water Watch (2023) 13 Groups Sue EPA Over Factory Farm Water Pollution. https://www.foodandwaterwatch.org/2023/09/11/13-groups-sue-epa-over-factory-farm-water-pollution/
Effluent Guidelines Program Plan 15, p. A-3.
U.S. EPA (January 13, 2025) Animal Agriculture and Water Quality (AAWQ) Subcommittee of Farm, Ranch, and Rural Communities Federal Advisory Committee. https://www.epa.gov/faca/frrcc-0 [see member list]
States can enact their own laws and regulations, including setting definitions for CAFOs that are broader in scope than those of the EPA.[1] They may also require additional conservation practices as part of a CAFO’s Nutrient Management Plan (NMP), especially in geographic areas like watersheds, where pollutants are more likely to flow into streams and rivers.[2]
But it is the NPDES program that drives most of the states’ laws regarding the discharges of manure from animal feeding operations.[3] The state regulations may be more stringent than EPA guidelines but not less so.[4] Every state except New Hampshire, Massachusetts, and New Mexico administers at least part of the NPDES program and has enacted state laws and regulations for doing so.
U.S. EPA (2012) NPDES Permit Writers’ Manual for Concentrated Animal Feeding Operations, EPA 833-F-12-001, p. 2-5.
NPDES Permit Writers’ Manual, p. 3-9
Peggy Hall & Ellen Essman (2019). USDA, National Agricultural Law Center, State Legal Approaches to Reducing Water Quality Impacts from the Use of Agricultural Nutrients on Farmland, p. 7. https://nalcpro.wpenginepowered.com/wp-content/uploads//assets/articles/agnutrient_report.pdf [This report offers an excellent overview of state regulations and approaches to agricultural nutrients and water quality]
40 CFR § 123.25 Requirements for permitting
Most states rely on guidelines for best managements practices which are difficult to monitor or regulate, particularly from nonpoint sources.[1,2]
Moreover, states also have the freedom to enact legislation that protects animal ag polluters. In 2024, Oklahoma signed into law a bill that shields poultry corporations from lawsuits over pollution caused by chicken waste as long as the poultry company has an approved state plan on how to dispose of the waste.[3] Yet the adequacy of state plans has been challenged. In a lawsuit against Tyson Foods and other poultry companies brought prior to the Oklahoma legislation, the defendant’s own scientific witness “acknowledged that the waterways remained impaired based on state standards.”[4]
Other challenges to pollution control by states and municipalities include lawsuits brought by the animal ag industry when they have been denied permits to expand due to environmental threats.[5]
Rosov, K.A., et al., (2020). Waste nutrients from U.S. animal feeding operations: Regulations are inconsistent across states and inadequately assess nutrient export risk. Journal of Environmental Management, 269, 110738–110738, p. 9. [“While scientific evidence clearly demonstrates damaging water quality consequences from CAFO waste disposal practices, there are few, if any, quantitative, empirical federal or state-sponsored analyses of manure nutrient exports.”]
Centner, T. (2012). Regulating the land application of manure from animal production facilities in the USA. Water Policy, 14(2), 319–335, p. 321. [“states have had difficulties in establishing appropriate controls for nonpoint-source pollution, and federal law contains no effective way to enforce BMPs.”]
Ben Felder (June 10, 2024) Oklahoma governor signs bill shielding poultry companies from lawsuits over chicken litter pollution. Investigate Midwest. https://investigatemidwest.org/2024/06/10/oklahoma-governor-signs-bill-shielding-poultry-companies-from-lawsuits-over-chicken-litter-pollution/
Ben Felder (December 26, 2024) Oklahoma AG’s expert witnesses push chicken waste ban amid federal lawsuit. Investigate Midwest. https://investigatemidwest.org/2024/12/26/oklahoma-ag-expert-witnesses-push-chicken-waste-ban-amid-federal-lawsuit/ [The lawsuit was based on the increasing amounts of chicken litter used as fertilizer that washed into nearby waterways, elevating phosphorus levels that turned water cloudy and strained the nearly 20 utility systems that rely on the Illinois River Watershed for drinking water.]
John McCracken (Sept. 4, 2024) Wisconsin towns are trying to limit CAFO growth. Big Dairy is fighting back, Investigate Midwest. https://investigatemidwest.org/2024/09/04/wisconsin-towns-are-trying-to-limit-cafo-growth-big-dairy-is-fighting-back/
Yes. Effective 2004, slaughterhouses and meat and poultry processors are considered “point sources” by the EPA and must achieve certain effluent limitations in their discharge of wastewater to waters of the U.S.[1-3]
However, an EPA review in 2021 found that the Meat and Poultry Processing (MPP) industry, amongst other problems, discharges the highest phosphorus levels and second highest nitrogen levels of all industrial categories, and nearly half of the direct discharge facilities were sending their wastewater to rivers and streams listed as impaired.[4] Following this review, the EPA has proposed more stringent effluent limitations for MPP facilities.[5]
40 CFR Part 432, Meat and Poultry Point Source Category
69 Fed Reg. 54476 Effluent Limitations Guidelines and New Source Performance Standards for the Meat and Poultry Products Point Source Category
For regulations on slaughterhouse and meat processing water discharges, see Slaughterhouse Water Regulations.
U.S. EPA (Sept. 2021) Preliminary Effluent Guidelines Program Plan 15, EPA-821-R-21-003, p. 6.2-6.3
89 Fed Reg. 4474 (January 23, 2024) Proposed Rules / Clean Water Act Effluent Limitations Guidelines and Standards for the Meat and Poultry Products Point Source Category. [“EPA is considering a range of options in this rulemaking. The options include more stringent effluent limitations on total nitrogen, new effluent limitations on total phosphorus, updated effluent limitations for other pollutants, new pretreatment standards for indirect dischargers, and revised production thresholds for some of the subcategories in the existing rule.” at p. 4475]